My system is showing the same output behavior (reasonable values for all
four observables except for PRESSURE), though I am not using molly.

I am using a script (attached) from a Prof. in our lab, a script, which
works fine for his system (PRESSURE values fluctuate around 1 bar).

However, my system (250K atoms) is much larger than his (80K atoms). Is
that the possible reason for the difference in PRESSURE output?

I am using both NAMD 2.6 and 2.7

Thank you,
Sebastian

Have you tried without MOLLY? It is a seldom-used option and I know it
has caused pressure problems in the past. You'll want to reduce your
fullelectfreq to compensate for turning it off...

As far as the actual pressure of your system, you need to take a long
timescale average of one of the pressure fields (PRESSAVG or GPRESSAVG
are good choices) *after* your system has equilibrated, which yours
certainly has not until near the end of your run, and possibly not even
then.